Confusion Among the Stars
by NerdInABlueBox
Summary: Kronos kidnaps Rory in hopes of gaining the Waverider and all of its crew, much to Rory's confusion of course. The Doctor and Amy along with the legends and the real Rip Hunter team up to rescue him. Together, they will reveal Kronos's true identity, and stop him for good.
1. Chapter 1

**Hello, it's me...Logan of the Lamp bringing you yet another crossover. Unlike my other two or three, this one is completely different. COMPLETELY. This is mainly due to the fact that I'm using DC's Legends of Tomorrow combined with the 11thDoctor. That's right, not the 10th, the 11th. Crazy right? I think it is fair to warn you that since Legends is so new, I may not get all the characters exactly right. If you have some pointers, tell me :D! I also have never written the 11th doctor, but I'm sure I'll grow accustomed pretty quickly, just gimme a chance :)**

 **Disclaimer: I do not own Legends of Tomorrow or Doctor who. If I did, I would buy a yacht, 'cause yachts are cool...so are bowties. Ya, those belong to DC and BBC**

 **Enjoy!**

* * *

Rory was the first to hear the slow churning of the TARDIS as it landed. He sat up, head still groggy from the little sleep he had managed to get. Amy was next. Her eyes opened and she looked up at her husband.

"Well, we better be getting dressed then." stated Rory.

"Why does he pick the worst times for our adventures?" wondered Amy.

"I honestly do not know." said Rory, as he grabbed a t-shirt from a drawer. He sat on the edge of the bed, feet hanging off as he pulled a t-shirt over his bare chest. "I'll meet him, you get dressed and stuff, then we'll head off I guess."

"Be sure to yell at him for coming this early." said Amy.

"Sure thing." replied Rory. He looked at the digital clock sitting on their nightstand. It read "4:09." Rory groaned and stood up off the bed, then started stumbling off towards the door of the bedroom.

"Pants." reminded Amy.

Rory grabbed his trousers and held them up for Amy to see as he left the bedroom.

Right as he left, a crash came from the living room along with several grunts and a yelp.

Amy sat up, definitely awake now. "Rory?"

"Ya?"

"What was that?"

Rory poked his head back into the room. "Umm, that came from downstairs."

"Someone's breaking in?" asked Amy, now scared.

"Remember, the Doctor is here. We heard the TARDIS. He probably just...did something. Like always."

"Can you check?" asked Amy.

"On my way down." Rory gave Amy a reassuring smile, and once again made off.

Amy sat up and started to get dressed, going as fast as she could.

She came into the living room, startled as she saw both the Doctor and Rory with their hands up, facing what seemed to be a robot of some kind. She took in a quick breath when she saw that the robot man was holding a futuristic looking gun at them. She heard the Doctor talking to him in a soothing tone. She hid behind a counter and listened, fearful of what could happen to her husband...or the Doctor.

"You don't have to do this, there are other ways of getting what you want. We can always talk. You and me, you really don't need to involve the peaceful inhabitants of this home."

"Who are you?" asked the robot, but his voice didn't sound robotic. _Okay, maybe not a robot, maybe a man-a pretty big man in a robotic-like suit...or is that armor? t_ hought Amy.

"I'm the Doctor. Who are you?" asked the Doctor.

"I'm Kronos...Doctor who?"

"Oh I love it when people ask me that, would you mind saying it again?"

"Yes, I do mind...I have no use for you, so how bout this instead?" Amy let out a strangled sound when Kronos shot the Doctor. The Doctor gasped as he collapsed to the floor, clutching his stomach. Now his back was to Kronos, who still had not noticed Amy. Meanwhile, Rory has, and had started to inch away from her so that Kronos definitely did not notice her.

Rory was fuming. Enraged, he brought his head up from the Doctor and turned to Kronos. "You didn't have to kill him!"

"Sadly he's not dead. This weapon isn't actually lethal, and all it does is deliver terrible pain, and most likely 3rd degree burns, but that's beside the point. You thought you could hide from me, Rip, in the past no less, but I still found you. And I now have all I need to attain the Waverider."

"What?" Rory's hand was behind him. _What is he doing?_ Amy then realized that the Doctor's sonic screwdriver was in his hand. Rory kept nervously glancing at the Doctor. He couldn't tell if he was okay or not.

"You're coming with me." said Kronos, as he took a step closer to Rory. Amy looked down at the Doctor, praying that he would do something. It was then that she realized that the Doctor was already looking at Amy. He nodded his head to Rory, and Amy knew what they were planning. She made eye contact with Rory and they came to an understanding.

Amy yelled, "Rory! Now!"

Rory threw the screwdriver at Amy as Kronos hit Rory in the head with the back of his gun-like weapon. She didn't know what to do with it, so she pointed it at Kronos as he started leaving the house and said, "let my husband go, or...or I will...use this on you!" Kronos stopped and turned his head to her. her as he picked up Rory and started to leave. She activated the screwdriver while pointing it at Kronos's head. Kronos stopped halfway out the door.

"Husband huh? I guess Rip has been busier than I thought." He resumed his trudge out the door as her as Amy activated the screwdriver while pointing it at Kronos's head. He paused when smoke started puffing from his helmet.

Rory came to not to long after Kronos had so rudely knocked him on the head with the bud of his weapon. All Rory could see was the door and Amy pointing the screwdriver at Kronos's head. Rory also saw the TARDIS parked a couple of feet away from him. He was now just standing there. Rory wasn't able to see Amy's face nor could he see the Doctor. The screwdriver seemed to be having an effect on Kronos, but then Kronos brought his hand up, pressing a button that revealed his face. Rory didn't recognize him...then again, he _was_ upside down and had a major headache. Rory noticed grey smoke float up and into the atmosphere as Kronos's face appeared. He didn't seem mad, but instead annoyed. Kronos looked at his wrist, but Rory couldn't tell what he was doing. Thankfully, Amy was wondering the same thing.

"W-what are you doing?" She was trying to sound brave but it didn't seem to be working.

"Just checking to see how important you are to the timeline." Kronos stood for a second longer, then said, "Oh wow, haven't seen readings like this...ever."

"And what is that supposed to mean?" questioned Amy.

Kronos looked back up into the house. "That means that I can't kill either of you. Stunning pain it is then!" Kronos brought his weapon up, and fired three times into the house.

"No! Amy!" screamed Rory. He struggled out of Kronos's grip and landed on the grass surrounding the back of his house. He made to run inside, but heard the weapon go off again and he stopped. It was at him this time. The last thing he remembered was Amy crying his name as he was dragged into Kronos's ship.

* * *

Amy shouted Rory's name over and over as the armored man dragged him away. She still didn't understand why this had happened. Why to them? And why did the Doctor have to jump in front of her when Kronos shot at them? She stared at his unconscious body, unsure of what to do. Kronos had hit him three times in total. One had missed and had gone into the wall behind them. Amy looked him over. He seemed to have gotten hit twice in the back and once at his chest. He didn't seem to be bleeding, for the weapon was firing what looked like laser beams. She examined the wounds. They weren't too bad. None had hit his spine. They weren't too deep. Amy closed her eyes for a second. _It's gonna be okay. It's gonna be okay._ She opened her eyes when she heard the Doctor groan.

"Doctor?" She crouched down next to him. His eyes were still closed. _Alright Amy, think. What would the Doctor do? What would...what would Rory do?_ She decided to get Rory's medical kit, clean and patch the Doctor's wounds, and then wait for him to wake up. Amy ran up to the second floor, and pulled Rory's first aid kit from the drawer. After that, she rushed downstairs to help the Doctor.

 _What did Rory say to do if the patient had a burn?_ wondered Amy. " _Run water over it to clean it, and then patch it up and wait for someone medically trained to help further." came Rory's soothing voice in her head._ Oh how she missed him. _He's gonna be fine_ she kept telling herself, but she couldn't help but worry.

Amy first carefully undid the Doctor's bowtie, and gently took it off of him. It was laid ceremonially next to him. She then slipped the Doctor's beloved tweed jacket off his body and placed it on the table, revealing his tan dress shirt and suspenders. _OI hope he doesn't hate me for this._ She pulled his suspenders off of his shoulders, and started unbuttoning his shirt.

Once all of the wounds were washed out and bandaged, she carefully brought him to the couch. She had to half drag, half carry him, for he was still unconscious, and very heavy. _How is he possibly this heavy?_ She set him down, and propped him on his side. That way, he would be the most comfortable. Amy went upstairs to get herself cleaned up. Hopefully, once the Doctor was awake again, he could help her find Rory.

* * *

Rory woke in a small cell. His hands were bound and his side was burning. He looked around him, wondering where Kronos was. He stood up, and walked to the door. It was open. _What kind of idiot would keep their prisoner in an open cell?_ He put his foot against the opening to see if he could walk through it, but was surprised when he got a minor shock and when the entire opening turned bright white for a split second. _Should have guessed._ He started pacing his celling, getting more bored with every minute. His thoughts had entirely consumed him. _Where was Amy and the Doctor now? Is Amy okay? Are they alive? If they are, when are they coming to get me?_ He snapped out of it when he heard the sound of a force field powering down. Kronos entered his cell.

"Follow me." said Kronos.

"No! First, you tell me where I am, if my wife and the Doctor are okay, and then maybe I will."

Kronos ignored this, and took Rory's arm. He tried to pull away but Kronos had an iron grip. After struggling for a bit, Rory decided to comply. After all, Kronos wouldn't hurt him, otherwise, he already would've.

After being guided through various rooms and hallways, Kronos pushed him into what looked like the control room. Kronos then guided Rory in front of a monitor, and positioned him in front of it.

"What is the point of this?" asked Rory.

"Your gonna tell your little gang of rebels to hand the Waverider and themselves over to me." ordered Kronos.

"Who and what, exactly?" asked Rory.

"I think you understand what I mean," said Kronos, as he pointed his gun at Rory. "Just so you know, I switched this to lethal."

Rory really didn't like where this was headed.

* * *

 **I hope you enjoyed this. Tell me if you did in the reviews and stuff because I love reviews! I made this during periods of writer's block for Identity Crises, but you know, I enjoyed writing this very much. I'm trying new things! Alright, cool, I appreciate it very much if you read this, so thanks for reading.**

 **Until next time...**

 **-The Lamp**


	2. Chapter 2

The Doctor woke with a start. Groaning, he attempted to sit up. To his right, he heard Amy say, "Oh no you don't!" And he felt warm hands lowering him back onto the couch.

"Amy?"

"Hello there raggedy man, I was afraid I was going to lose you for a second there."

"And why is that?" Then the pain hit him. It had been there before, he just hadn't noticed it. He looked down to see a blanket covering his body. The Doctor pulled it away to find bandages covering him from his waist to just below his armpits, and an extra wrapped around his left arm. He groaned again, letting his head rest on a pillow behind him. "I should be dead" he muttered.

"And why is that?" asked Amy

"Well I got shot about three times and-"

"Four actually"

"Well alright, four times, and I probably should have bled out and regenerated by now."

Amy decided to ignore the last part due to the fact that she didn't understand what he meant by "regenerating."

"It was some weird laser blast. It didn't go too deep, just a really bad burn. I took care of the little blood there was."

"Well, that's a relief."

"I cleaned them and bandaged them, but that's all I knew how to do. Rory taught me-"

"Rory...RORY where is he?!" asked the Doctor.

"Kronos took him and tried to shoot me. Don't you remember?"

"Not very well. Did you see where he was taken? How about who took him?" questioned the Doctor.

"No, I was too busy freaking out after you jumped in front of me like that!"

"No matter, I assume I had a plan." The Doctor thought for a minute.

"Typical. The man with the plan. Yep, that's the Doctor." ranted Amy.

The Doctor ignored this as Amy started pacing back and forth, talking about how much she needed Rory back and how much of an idiot he was for getting himself hurt.

"Oh I remember now! I had you sonic them right?" exclaimed the Doctor.

"Kind of, Rory actually threw it to me."

"Point is, you sonic-ed Kronos right?"

"Ya, his helmet started smoking."

"Well if we're really lucky, the sonic scanned or damaged his navigation and main control systems. If you did that, the navigation one I mean, I can probably track them on my TARDIS." As he said this, he sat up, grimacing, but Amy didn't notice.

"Oh thank god...Do you think he's okay?"asked Amy

"I'm sure he's fine." replied the Doctor.

Amy didn't seem too convinced.

"Alright let's go." said the Doctor. He sprang up from his seated position and tried to take a step forward. He immediately regretted as his legs gave out. Luckily, Amy was there to catch him.

"Doctor..."

"I'm alright!" exclaimed the Doctor with a smile. Amy wasn't convinced. With Amy's help, he steadily got to his feet, hiding the pain from the movements. The Doctor then clasped his hands and spun around to face Amy, still smiling. "Where's my shirt?" he asked.

Amy handed the beige button-up shirt to him.

"Bowtie?"

Amy carefully handed it to him. She knew how he was with them.

After his bowtie was secure, he found his tweed jacket hanging on the back of a chair, put it on, and headed for the back door. Amy followed.

The TARDIS stood, old and blue as ever. The Doctor and Amy entered.

"Do you have my screwdriver?" asked the Doctor.

"Ya, here." Amy handed the contraption to him.

"Thank you." The Doctor took the screwdriver started fiddling with the console, occasionally buzzing the screwdriver. He found various readings and this and that and eventually put the trace from the screwdriver transferred onto the console.

Amy walked over to the pilot's seat and sat down, the whole day's events finally crashing down on her.

"Are you alright?" asked the Doctor, still busy with his piloting.

"Ya, thanks to you." admitted Amy.

"Well I couldn't have you getting killed now could I?" he smiled as he worked, and Amy did as well. Neither of them looked at each other and silence came over the two. The only sound in the room was the TARDIS and the sound of various console instruments being operated.

* * *

Sara was in the control room when the transmission came in. At first, it was Kronos.

"Rip!" she yelled. "Come here I think you want to see this!" When she looked back at the screen, Kronos was no longer there. Instead, in his place was...Rip?

"Rip?" asked Sara, "Rip what are you doing there?"

Right then, Ray, Kendra and Leonard ran in, who were all wondering what was going on.

The Rip on the screen started speaking. "Hello...all. You will hand over all of yourselves along with the..tide rider-" Kronos punched Rory across the face, drawing blood from his nose which then started trickling down his face. Something was said off screen, and Rory looked back to the camera.

"Right, w-waverider...immediately otherwise he will probably kill me."

"You idiot. Move aside." Kronos proceeded to wrap a hand around Rory's arm, point his gun at his head and looked into the camera. I will shoot your captain if you don't hand over the waverider and your entire crew of freaks to myself and the time masters at the coordinates I will send to you. Be there at 0500, otherwise he dies."

The screen went black after that.

Rip jogged into the room, coat flapping behind him.

"I'm here, what is it?" asked Rip.

"You were just on the screen, and Kronos had you and punched you and demanded we hand ourselves and the Waverider over to the time masters otherwise you will die! Is that your younger self? Future self? Twin? Another family member? He looked exactly like you! How is that even possible?" said Ray.

"Ray, slow down. What's happening? Was I on the screen?"

"Yes, but I assume since your standing here that it probably wasn't you." stated Snart.

"Well that's complicated, me being a time traveler and all that."

Rip was interrupted when Gideon spoke.

"I have received coordinates from Kronos, Mr. Hunter. Would you like for me to enter them?" asked Gideon.

"Yes." said Rip.

"What?" exclaimed Sara. "You're just going to hand us over?"

"Of course not, we board his ship, rescue myself, and leave. The Time Masters wouldn't give kronos any assistance, otherwise he would have attacked this ship already. He's on his own."

Jax and Stein walked into the control room.

"Well he clearly knows where we are. That's how he got the coordinates sent to us. He's on his own, and we should easily be able to overtake him. But if we're not careful he could attack the waverider." said Rip.

"I'm sorry, what's happening?" asked Jax.

"Long story short, Rip just appeared on the screen and through him, Kronos wants us to hand over the waverider and ourselves, which is definately not happening. So we're planning on taking Kronos's ship and rescuing Rip." summarized Sara.

"But then we're risking losing you." said Kendra

"That's not really me. Time can change." said Rip.

"But if that you dies, will you cease to exist?"

"Not necessarily."

"What's that supposed to mean?" asked Snart

"It doesn't matter because that's not happening. We need to go. Now."

* * *

"C'mon Rip, why act dumb in this situation? There is no reason for that! They'll come either way."

"Sir, I have absolutely no idea who 'they' or even you, for that matter, are. I don't know what a 'waverider' is. Why am I here? And how do they supposedly know who I am?"

"Don't play stupid." Kronos yanked on Rory's collar to get him standing, and started walking back to his holding cell.

"My name isn't even Rip!"

Kronos ignored this and kept walking down the hall, still dragging Rory. His side still stung from getting shot. He looked down to see that some blood was seeping through his collared shirt.

Finally, they reached the cell. Kronons pushed him in. Afterwards, he reenabled the door of electricity to ensure that Rory would not escape. He sat down on the cold metal floor and started thinking. ' _Where are you doctor?'_. Yes, the Doctor would come to save him. He always did.

 **Alright so not my best, but hey, at least I posted :)**

 **Leave a review and you get a papaya!**


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